Abstract 4028: Menin inhibitor-based combinations to improve efficacy and overcome resistance in AML
Authors: Warren C. Fiskus, Christopher P. Mill, Christine Birdwell, John A. Davis, Qi Jin, Tapan M. Kadia, Courtney D. DiNardo, Koichi Takahashi, Gerard M. McGeehan, Naval Daver, Kapil N. Bhalla
Journal: Cancer Research (2022)

Abstract In MLL1 rearranged (MLL1r) AML (~10%), N-terminus of MLL1 gene is fused to the C-terminus of a fusion partner, e.g. AF9, AF4, ENL and ELL, creating MLL1 fusion protein (MLL-FP), which increases expression of leukemogenic HOXA9 and its co-factor MEIS1. In AML with mutant (mt) NPM1 (NPM1c), MLL1 is the main driver of HOXA9, MEIS1 and FLT3, promoting self-renewal and growth of AML stem-progenitor cells (LSCs). Treatment with Menin inhibitor (MI), SNDX-50469 or SNDX-5613, disrupts binding of Menin to its binding pocket in MLL1/2 and MLL1-FP, reducing expressions of their targets and inducing differentiation and apoptosis. In the phase I/II AUGMENT-101 clinical trial, SNDX-5613 monotherapy was well tolerated and achieved objective remissions in patients with previously treated relapsed/refractory AML harboring MLL1r or NPM1c. However, majority of patients either fail to respond or eventually relapse. A minority of MLL1r AML (~9%) also exhibit a co-mutation in TP53, which is known to confer therapy resistance and poor outcome in AML. This creates the need to develop MI-based synergistic combinations with superior efficacy against patient-derived (PD) AML cells harboring MLL-FP or NPM1c. Present studies found that, following MI treatment, CyTOF analysis of PD MLL1-r and NPM1c AML cells showed decline in protein levels of Menin, MEIS1, MEF2C, PBX3, FLT3, CDK6 and BCL2 in phenotypically characterized AML LSCs expressing CLEC12A, CD123, CD244 and CD99. Notably, in vitro co-treatment with SNDX-50469 in combination with venetoclax, OTX015 (pan-BET inhibitor) or abemaciclib (CDK6 inhibitor) induced synergistic (determined by SynergyFinder V2) loss of viability in AML cell lines (MV4-11, MOLM13 and OCI-AML3), as well as in MOLM13 cells with CRISPR-Cas9-mediated knock-in of mutant or allelic loss of TP53 and in PD AML cells with MLL-r or NPM1c, but not in normal CD34+ progenitor cells or AML cells lacking MLL-FP or NPM1c. A CRISPR screen with a validated, domain-specific gRNA library against chromatin regulators revealed BRD4, p300, MOZ and KDM1A as druggable co-dependencies with treatment with MI. Consistent with this, co-treatment with SNDX-50469 and OTX015, or the p300/CBP inhibitor GNE049 was synergistically lethal in vitro in AML cells with MLL1r or NPM1c, either sensitive to MI or tolerant-resistant (induced in vitro) to MI (MITR cells). Co-treatment with SNDX-5613 and venetoclax or OTX015 compared to each drug or vehicle control, administered orally for 3 to 4 weeks to NSG mice engrafted with either MOLM13-GFP/Luciferase xenograft or with PD NPM1c and mtFLT3 AML xenograft, caused significantly greater reduction in AML burden and increased overall survival without weight loss or other toxicities (p &amp;lt; 0.005). These preclinical findings highlight novel MI-based combinations exhibiting superior in vitro and in vivo anti-AML efficacy against AML cells harboring MLL1-FP or NPM1c that are sensitive to MI or the MITR cells. Citation Format: Warren C. Fiskus, Christopher P. Mill, Christine Birdwell, John A. Davis, Qi Jin, Tapan M. Kadia, Courtney D. DiNardo, Koichi Takahashi, Gerard M. McGeehan, Naval Daver, Kapil N. Bhalla. Menin inhibitor-based combinations to improve efficacy and overcome resistance in AML [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 4028.